On 10/12/2011 6:25 AM, neeru sharma wrote:
Dear gromacs users,
I have to simulate a protein-GDP complex using gromacs.As PRODRG was
giving unreliable output, I generated Amber topology and coordinate
files for GTP molecule. Then, I converted them into the corresponding
gromacs topology (.top) and coordinate files (.gro) and generated
parameter (.itp) file using following command (Thanks to Tsjerk):
sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP > ITP
But the topology and co-ordinates file are quite different from the
input PDB file and hence the parameters are also faulty, the GDP
molecule is not fitting in the binding pocket of protein. Upon
tracking the whole process, it was found that the error might be while
using antechamber for generating prepin file using Gaussian output
file as the input.
Can anyone please suggest some way to apply some constraints in the
antechamber command itself. OR if anybody has the paramters or
topology for GDP, can anyone provide me the same so that I can compare
and see where the parameters are differing.
Surely antechamber will accept whatever coordinate file you provide to
it, and the AMBER mailing list is the place to make inquiries about it
(after checking the documentation).
Don't stress too much about the charges - those that are suitable in the
bound and unbound form will normally be different, and current methods
can't access the former.
Mark
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